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Wang K, Cunha GM, Hasenstab K, Henderson WC, Middleton MS, Cole SA, Umans JG, Ali T, Hsiao A, Sirlin CB. Deep Learning for Inference of Hepatic Proton Density Fat Fraction From T1-Weighted In-Phase and Opposed-Phase MRI: Retrospective Analysis of Population-Based Trial Data. AJR Am J Roentgenol 2023; 221:620-631. [PMID: 37466189 DOI: 10.2214/ajr.23.29607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
BACKGROUND. The confounder-corrected chemical shift-encoded MRI (CSE-MRI) sequence used to determine proton density fat fraction (PDFF) for hepatic fat quantification is not widely available. As an alternative, hepatic fat can be assessed by a two-point Dixon method to calculate signal fat fraction (FF) from conventional T1-weighted in- and opposed-phase (IOP) images, although signal FF is prone to biases, leading to inaccurate quantification. OBJECTIVE. The purpose of this study was to compare hepatic fat quantification by use of PDFF inferred from conventional T1-weighted IOP images and deep-learning convolutional neural networks (CNNs) with quantification by use of two-point Dixon signal FF with CSE-MRI PDFF as the reference standard. METHODS. This study entailed retrospective analysis of data from 292 participants (203 women, 89 men; mean age, 53.7 ± 12.0 [SD] years) enrolled at two sites from September 1, 2017, to December 18, 2019, in the Strong Heart Family Study (a prospective population-based study of American Indian communities). Participants underwent liver MRI (site A, 3 T; site B, 1.5 T) including T1-weighted IOP MRI and CSE-MRI (used to reconstruct CSE PDFF and CSE R2* maps). With CSE PDFF as reference, a CNN was trained in a random sample of 218 (75%) participants to infer voxel-by-voxel PDFF maps from T1-weighted IOP images; testing was performed in the other 74 (25%) participants. Parametric values from the entire liver were automatically extracted. Per-participant median CNN-inferred PDFF and median two-point Dixon signal FF were compared with reference median CSE-MRI PDFF by means of linear regression analysis, intraclass correlation coefficient (ICC), and Bland-Altman analysis. The code is publicly available at github.com/kang927/CNN-inference-of-PDFF-from-T1w-IOP-MR. RESULTS. In the 74 test-set participants, reference CSE PDFF ranged from 1% to 32% (mean, 11.3% ± 8.3% [SD]); reference CSE R2* ranged from 31 to 457 seconds-1 (mean, 62.4 ± 67.3 seconds-1 [SD]). Agreement metrics with reference to CSE PDFF for CNN-inferred PDFF were ICC = 0.99, bias = -0.19%, 95% limits of agreement (LoA) = (-2.80%, 2.71%) and for two-point Dixon signal FF were ICC = 0.93, bias = -1.11%, LoA = (-7.54%, 5.33%). CONCLUSION. Agreement with reference CSE PDFF was better for CNN-inferred PDFF from conventional T1-weighted IOP images than for two-point Dixon signal FF. Further investigation is needed in individuals with moderate-to-severe iron overload. CLINICAL IMPACT. Measurement of CNN-inferred PDFF from widely available T1-weighted IOP images may facilitate adoption of hepatic PDFF as a quantitative bio-marker for liver fat assessment, expanding opportunities to screen for hepatic steatosis and nonalcoholic fatty liver disease.
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Affiliation(s)
- Kang Wang
- Department of Radiology, Artificial Intelligence and Data Analytic Laboratory, University of California, San Diego, La Jolla, CA
- Department of Radiology, Liver Imaging Group, University of California, San Diego, La Jolla, CA
- Department of Radiology, Stanford University, 500 Pasteur Dr, Palo Alto, CA 94304
| | | | - Kyle Hasenstab
- Department of Radiology, Artificial Intelligence and Data Analytic Laboratory, University of California, San Diego, La Jolla, CA
- Department of Radiology, Liver Imaging Group, University of California, San Diego, La Jolla, CA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA
| | - Walter C Henderson
- Department of Radiology, Liver Imaging Group, University of California, San Diego, La Jolla, CA
| | - Michael S Middleton
- Department of Radiology, Liver Imaging Group, University of California, San Diego, La Jolla, CA
| | - Shelley A Cole
- Population Health, Texas Biomedical Research Institute, San Antonio, TX
| | - Jason G Umans
- MedStar Health Research Institute, Field Studies Division, Hyattsville, MD
- Georgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC
| | - Tauqeer Ali
- Department of Biostatistics and Epidemiology, Center for American Indian Health Research, Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Albert Hsiao
- Department of Radiology, Artificial Intelligence and Data Analytic Laboratory, University of California, San Diego, La Jolla, CA
| | - Claude B Sirlin
- Department of Radiology, Liver Imaging Group, University of California, San Diego, La Jolla, CA
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Contribution of genetic, biochemical and environmental factors on insulin resistance and obesity in Mexican young adults. Obes Res Clin Pract 2019; 13:533-540. [PMID: 31796261 DOI: 10.1016/j.orcp.2019.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 09/29/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022]
Abstract
Overweight/obesity, dyslipidemias, hypertension and hyperglycemia are strongly related to non-communicable diseases (NCD) in which genetic and environmental factors interact with each other. The Mexican population exhibit a genetic disposition to metabolic syndrome, type 2 diabetes, as well as many forms of dyslipidemia. This study aimed to determine the association between biochemical, genetic and environmental factors in the development of metabolic syndrome (MS), obesity and insulin resistance (IR) in Mexican young adults. Young women and men (n=6750 between 19.3±2.3 years old) participated in a health promotion program from the Autonomous University of Querétaro, México (SU-Salud program). A sub-sample of 665 participants was taken for the determination of single nucleotide polymorphisms (SNP) rs964184 (APOAV), rs9282541 (ABCA1) and rs1260326 (GCKR), using QuantStudio 12K Flex Real-Time PCR System. For the multivariate analysis, a multiple logistic regression was performed. A prevalence of 22% of overweight and 7% of obesity was determined. The main metabolic risk factors were low levels of HDL-C (30%), IR (19%), and a high level of triglycerides (15%). The main factors associated with IR were body fat percentage and triglycerides; SNP for the ABCA1 gene was related to MS, obesity and low HDL-C; SNP for GCKR gene was related to high fasting glycemia, while APOAV SNP was related with MS, hypertriglyceridemia and low HDL-C. Our findings show that the Mexican genetic predisposition to NCD affects young adults, who can suffer MS, obesity and IR. Public health strategies must focus on prevention actions from an early age.
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Justice AE, Howard AG, Fernández-Rhodes L, Graff M, Tao R, North KE. Direct and indirect genetic effects on triglycerides through omics and correlated phenotypes. BMC Proc 2018; 12:22. [PMID: 30275878 PMCID: PMC6157130 DOI: 10.1186/s12919-018-0118-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Even though there has been great success in identifying lipid-associated single-nucleotide polymorphisms (SNPs), the mechanisms through which the SNPs act on each trait are poorly understood. The emergence of large, complex biological data sets in well-characterized cohort studies offers an opportunity to investigate the genetic effects on trait variability as a way of informing the causal genes and biochemical pathways that are involved in lipoprotein metabolism. However, methods for simultaneously analyzing multiple omics, environmental exposures, and longitudinally measured, correlated phenotypes are lacking. The purpose of our study was to demonstrate the utility of the structural equation modeling (SEM) approach to inform our understanding of the pathways by which genetic variants lead to disease risk. With the SEM method, we examine multiple pathways directly and indirectly through previously identified triglyceride (TG)-associated SNPs, methylation, and high-density lipoprotein (HDL), including sex, age, and smoking behavior, while adding in biologically plausible direct and indirect pathways. We observed significant SNP effects (P < 0.05 and directionally consistent) on TGs at visit 4 (TG4) for five loci, including rs645040 (DOCK7), rs964184 (ZPR1/ZNF259), rs4765127 (ZNF664), rs1121980 (FTO), and rs10401969 (SUGP1). Across these loci, we identify three with strong evidence of an indirect genetic effect on TG4 through HDL, one with evidence of pleiotropic effect on HDL and TG4, and one variant that acts on TG4 indirectly through a nearby methylation site. Such information can be used to prioritize candidate genes in regions of interest, inform mechanisms of action of methylation effects, and highlight possible genes with pleiotropic effects.
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Affiliation(s)
- Anne E Justice
- 1Department of Epidemiology, University of North Carolina, Chapel Hill, NC USA.,2Biomedical and Translational Informatics, Geisinger Health, Danville, PA USA
| | - Annie Green Howard
- 3Department of Biostatistics, University of North Carolina, Chapel Hill, NC USA.,4Carolina Population Center, University of North Carolina, Chapel Hill, NC USA
| | - Lindsay Fernández-Rhodes
- 1Department of Epidemiology, University of North Carolina, Chapel Hill, NC USA.,4Carolina Population Center, University of North Carolina, Chapel Hill, NC USA
| | - Misa Graff
- 1Department of Epidemiology, University of North Carolina, Chapel Hill, NC USA
| | - Ran Tao
- 5Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN USA
| | - Kari E North
- 1Department of Epidemiology, University of North Carolina, Chapel Hill, NC USA
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Arbour L, Asuri S, Whittome B, Polanco F, Hegele RA. The Genetics of Cardiovascular Disease in Canadian and International Aboriginal Populations. Can J Cardiol 2015; 31:1094-115. [DOI: 10.1016/j.cjca.2015.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 12/16/2022] Open
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Vaughan LK, Wiener HW, Aslibekyan S, Allison DB, Havel PJ, Stanhope KL, O'Brien DM, Hopkins SE, Lemas DJ, Boyer BB, Tiwari HK. Linkage and association analysis of obesity traits reveals novel loci and interactions with dietary n-3 fatty acids in an Alaska Native (Yup'ik) population. Metabolism 2015; 64:689-97. [PMID: 25772781 PMCID: PMC4408244 DOI: 10.1016/j.metabol.2015.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 01/30/2015] [Accepted: 02/28/2015] [Indexed: 12/25/2022]
Abstract
OBJECTIVE To identify novel genetic markers of obesity-related traits and to identify gene-diet interactions with n-3 polyunsaturated fatty acid (n-3 PUFA) intake in Yup'ik people. MATERIAL AND METHODS We measured body composition, plasma adipokines and ghrelin in 982 participants enrolled in the Center for Alaska Native Health Research (CANHR) Study. We conducted a genome-wide SNP linkage scan and targeted association analysis, fitting additional models to investigate putative gene-diet interactions. Finally, we performed bioinformatic analysis to uncover likely candidate genes within the identified linkage peaks. RESULTS We observed evidence of linkage for all obesity-related traits, replicating previous results and identifying novel regions of interest for adiponectin (10q26.13-2) and thigh circumference (8q21.11-13). Bioinformatic analysis revealed DOCK1, PTPRE (10q26.13-2) and FABP4 (8q21.11-13) as putative candidate genes in the newly identified regions. Targeted SNP analysis under the linkage peaks identified associations between three SNPs and obesity-related traits: rs1007750 on chromosome 8 and thigh circumference (P=0.0005), rs878953 on chromosome 5 and thigh skinfold (P=0.0004), and rs1596854 on chromosome 11 for waist circumference (P=0.0003). Finally, we showed that n-3 PUFA modified the association between obesity related traits and two additional variants (rs2048417 on chromosome 3 for adiponectin, P for interaction=0.0006 and rs730414 on chromosome 11 for percentage body fat, P for interaction=0.0004). CONCLUSIONS This study presents evidence of novel genomic regions and gene-diet interactions that may contribute to the pathophysiology of obesity-related traits among Yup'ik people.
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Affiliation(s)
- Laura Kelly Vaughan
- Department of Biology, King University, 1350 King College Rd, Bristol, TN 37620, USA.
| | - Howard W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35294, USA.
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35294, USA.
| | - David B Allison
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35294, USA.
| | - Peter J Havel
- Departments of Nutrition and Molecular Biosciences, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
| | - Kimber L Stanhope
- Departments of Nutrition and Molecular Biosciences, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
| | - Diane M O'Brien
- USACenter for Alaska Native Health Research, Institute of Arctic Biology, 311 Irving I Building, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Scarlett E Hopkins
- USACenter for Alaska Native Health Research, Institute of Arctic Biology, 311 Irving I Building, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Dominick J Lemas
- Department of Pediatrics, Section of Neonatology, University of Colorado Anschutz Medical Campus, 13123 East 16th Ave, Aurora, CO 80045, USA.
| | - Bert B Boyer
- USACenter for Alaska Native Health Research, Institute of Arctic Biology, 311 Irving I Building, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Hemant K Tiwari
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35294, USA.
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Wang W, Yin RX, Wu DF, Aung LHH, Huang P, Zeng XN, Huang KK, Lin QZ, Wu J, Guo T. Phosphodiesterase 3A rs7134375 single nucleotide polymorphism and serum lipid levels. Mol Med Rep 2014; 9:1618-28. [PMID: 24604378 PMCID: PMC4020489 DOI: 10.3892/mmr.2014.2007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 02/14/2014] [Indexed: 12/19/2022] Open
Abstract
The association between the phosphodiesterase 3A (PDE3A) rs7134375 single nucleotide polymorphism (SNP) and serum lipid levels are not well understood in the general population. The present study was performed in order to detect the association between the rs7134375 SNP and serum lipid levels in the Guangxi Mulao and Han populations. The genotypes of the PDE3A rs7134375 SNP in 761 subjects of the Mulao population and 774 subjects of the Han Chinese population were determined by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing. It was observed that serum low-density lipoprotein cholesterol and apolipoprotein B levels were higher in the Mulao population than in the Han population (P<0.05 for each). The frequencies of the C and A alleles were 72.14 and 27.86% in the Mulao population, and 78.55 and 21.45% in the Han population (P<0.01), respectively. The frequencies of the CC, CA and AA genotypes were 52.04, 40.21 and 7.75% in the Mulao population, and 61.50, 34.11 and 4.39% in the Han population (P<0.01), respectively. The frequencies of the C and A alleles were 74.89 and 25.11% in Mulao females, and 68.08 and 31.92% in Mulao males (P<0.01), respectively. The serum triglyceride (TG) levels were different among the genotypes in the Mulao population; however, not in the Han population (P<0.01), and the A allele carriers exhibited lower TG levels than the A allele noncarriers. The serum lipid parameters were also correlated with several environmental factors in the two ethnic groups (P<0.05-0.001). It was concluded that the genotypic and allelic frequencies of the rs7134375 SNP are different between the Mulao and Han populations. In addition, the PDE3A rs7134375 SNP is associated with serum TG levels in the Mulao population, however, not in the Han population.
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Affiliation(s)
- Wei Wang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Dong-Feng Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Lynn Htet Htet Aung
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Ping Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiao-Na Zeng
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Ke-Ke Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Quan-Zhen Lin
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jian Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Tao Guo
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Huang KK, Yin RX, Zeng XN, Huang P, Lin QZ, Wu J, Guo T, Wang W, Yang DZ, Lin WX. Association of the rs7395662 SNP in the MADD-FOLH1 and several environmental factors with serum lipid levels in the Mulao and Han populations. Int J Med Sci 2013; 10:1537-46. [PMID: 24046529 PMCID: PMC3775112 DOI: 10.7150/ijms.6421] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 08/12/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The rs7395662 single nucleotide polymorphism (SNP) in the MADD-FOLH1 has been associated with serum lipid traits, but the results are inconsistent in different populations. The present study was undertaken to investigate the association of rs7395662 SNP and several environmental factors with serum lipid levels in the Guangxi Mulao and Han populations. METHOD A total of 721 subjects of Mulao and 727 subjects of Han Chinese were randomly selected from our previous stratified randomized samples. Genotyping of the SNP was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and confirmed by direct sequencing. RESULTS Serum apolipoprotein (Apo) B levels were higher in Mulao than in Han (P < 0.01). The allelic and genotypic frequencies in Han were different between males and females (P < 0.05 for each), but there was no difference between Mulao and Han or between Mulao males and females. The levels of low-density lipoprotein cholesterol (LDL-C) and ApoB in Mulao females were different among the genotypes (P < 0.05), the G allele carriers had higher LDL-C and ApoB levels than the G allele non-carriers. The levels of total cholesterol (TC), triglyceride (TG), LDL-C and ApoB in Han males and TC, TG and high-density lipoprotein cholesterol (HDL-C) in Han females were different among the genotypes (P < 0.05-0.01), the subjects with GG genotype in Han males had higher TC, TG, and ApoB and lower LDL-C levels than the subjects with AA or AG genotype, and the G allele carriers in Han females had lower TC and HDL-C levels than the G allele non-carriers. The levels of LDL-C and ApoB in Mulao females were correlated with the genotypes (P < 0.05 for each). The levels of HDL-C and ApoAI in Han males and HDL-C in Han females were correlated with genotypes (P < 0.05-0.001). Serum lipid parameters were also correlated with several environmental factors in both ethnic groups (P < 0.05-0.01). CONCLUSION The association of rs7395662 SNP and serum lipid levels is different between the Mulao and Han populations, and between males and females in both ethnic groups.
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Affiliation(s)
- Ke-Ke Huang
- 1. Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, Guangxi, People's Republic of China
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Yan TT, Yin RX, Li Q, Huang P, Zeng XN, Huang KK, Aung LHH, Wu DF, Liu CW, Pan SL. Sex-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels in the Mulao and Han populations. Lipids Health Dis 2011; 10:248. [PMID: 22208664 PMCID: PMC3274493 DOI: 10.1186/1476-511x-10-248] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 12/31/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The association of rs16996148 single nucleotide polymorphism (SNP) in NCAN/CILP2/PBX4 and serum lipid levels is inconsistent. Furthermore, little is known about the association of rs16996148 SNP and serum lipid levels in the Chinese population. We therefore aimed to detect the association of rs16996148 SNP and several environmental factors with serum lipid levels in the Guangxi Mulao and Han populations. METHOD A total of 712 subjects of Mulao nationality and 736 participants of Han nationality were randomly selected from our stratified randomized cluster samples. Genotyping of the rs16996148 SNP was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing. RESULTS The levels of apolipoprotein (Apo) B were higher in Mulao than in Han (P < 0.001). The frequencies of G and T alleles were 87.2% and 12.8% in Mulao, and 89.9% and 10.1% in Han (P <0.05); respectively. The frequencies of GG, GT and TT genotypes were 76.0%, 22.5% and 1.5% in Mulao, and 81.2%, 17.4% and 1.4% in Han (P <0.05); respectively. There were no significant differences in the genotypic and allelic frequencies between males and females in both ethnic groups. The levels of HDL-C, ApoAI, and the ratio of ApoAI to ApoB in Mulao were different between the GG and GT/TT genotypes in males but not in females (P < 0.01 for all), the subjects with GT/TT genotypes had higher serum levels of HDL-C, ApoAI, and the ratio of ApoAI to ApoB than the subjects with GG genotype. The levels of TC, TG, LDL-C, ApoAI, and ApoB in Han were different between the GG and GT/TT genotypes in males but not in females (P < 0.05-0.001), the T allele carriers had higher serum levels of TC, TG, LDL-C, ApoAI, and ApoB than the T allele noncarriers. The levels of HDL-C, ApoAI, and the ratio of ApoAI to ApoB in Mulao were correlated with the genotypes in males (P < 0.05-0.01) but not in females. The levels of TC, TG, HDL-C, LDL-C, ApoAI and ApoB in Han were associated with the genotypes in males (P < 0.05-0.001) but not in females. Serum lipid parameters were also correlated with several enviromental factors in both ethnic groups (P < 0.05-0.001). CONCLUSIONS The genotypic and allelic frequencies of rs16996148 SNP and the associations of the SNP and serum lipid levels are different in the Mulao and Han populations. Sex (male)-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels is also observed in the both ethnic groups.
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Affiliation(s)
- Ting-Ting Yan
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Qing Li
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Ping Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xiao-Na Zeng
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Ke-Ke Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Lynn Htet Htet Aung
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Dong-Feng Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Cheng-Wu Liu
- Department of Pathophysiology, School of Premedical Sciences, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Premedical Sciences, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
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Hodoğlugil U, Williamson DW, Yu Y, Farrer LA, Mahley RW. Glucuronic acid epimerase is associated with plasma triglyceride and high-density lipoprotein cholesterol levels in Turks. Ann Hum Genet 2011; 75:398-417. [PMID: 21488854 DOI: 10.1111/j.1469-1809.2011.00644.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We narrowed chromosome 15q21-23 linkage to plasma high-density lipoprotein cholesterol (HDL-C) levels in Turkish families by fine mapping, then focused on glucuronic acid epimerase (GLCE), a heparan sulfate proteoglycan (HSPG) biosynthesis enzyme. HSPGs participate in lipid metabolism along with apolipoprotein (apo) E. Of 31 SNPs in the GLCE locus, nine analyzed by haplotype were associated with HDL-C and triglyceride levels (permuted p = 0.006 and 0.013, respectively) in families. Of five tagging GLCE SNPs in two cohorts of unrelated subjects, three (rs16952868, rs11631403, and rs3865014) were associated with triglyceride and HDL-C levels in males (nonpermuted p < 0.05). The association was stronger in APOE 2/3 subjects (apoE2 has reduced binding to HSPGs) and reached multiple-testing significance (p < 0.05) in both males and females (n= 2612). Similar results were obtained in the second cohort (n= 1164). Interestingly, at the GLCE locus, bounded by recombination hotspots, Turks had a minor allele frequency of SNPs resembling Chinese more than European ancestry; adjoining regions resembled the European pattern. Studies of glce(+/-) apoe(-/-) mice fed a chow or high-fat diet supported a role for GLCE in lipid metabolism. Thus, SNPs in GLCE are associated with triglyceride and HDL-C levels in Turks, and mouse studies support a role for glce in lipid metabolism.
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Affiliation(s)
- Uğur Hodoğlugil
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA
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Dong C, Beecham A, Wang L, Slifer S, Wright CB, Blanton SH, Rundek T, Sacco RL. Genetic loci for blood lipid levels identified by linkage and association analyses in Caribbean Hispanics. J Lipid Res 2011; 52:1411-9. [PMID: 21558551 DOI: 10.1194/jlr.p013672] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To identify genetic loci influencing blood lipid levels in Caribbean Hispanics, we first conducted a genome-wide linkage scan in 1,211 subjects from 100 Dominican families on five lipid quantitative traits: total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), triglycerides (TG), and LDL-C/HDL-C ratio. We then investigated the association between blood lipid levels and 21,361 single nucleotide polymorphisms (SNP) under the 1-logarithm of odds (LOD) unit down regions of linkage peaks in an independent community-based subcohort (N = 814, 42% Dominican) from the Northern Manhattan Study (NOMAS). We found significant linkage evidence for LDL-C/HDL-C on 7p12 (multipoint LOD = 3.91) and for TC on 16q23 (LOD = 3.35). In addition, we identified suggestive linkage evidence of LOD > 2.0 on 15q23 for TG, 16q23 for LDL-C, 19q12 for TC and LDL-C, and 20p12 for LDL-C. In the association analysis of the linkage peaks, we found that seven SNPs near FLJ45974 were associated with LDL-C/HDL-C with a nominal P < 3.5 × 10(-5), in addition to associations (P < 0.0001) for other lipid traits with SNPs in or near CDH13, SUMF2, TLE3, FAH, ARNT2, TSHZ3, ZNF343, RPL7AL2, and TMC3. Further studies are warranted to perform in-depth investigations of functional genetic variants in these regions.
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Affiliation(s)
- Chuanhui Dong
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
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Morris A, Ferdinand KC. Hyperlipidemia in racial/ethnic minorities: differences in lipid profiles and the impact of statin therapy. ACTA ACUST UNITED AC 2009. [DOI: 10.2217/clp.09.70] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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